In [1]:
library(Seurat)
library(dplyr)
library(magrittr)
IRdisplay::display_html("<style> .container { width:95% !important; } </style>")
library("xlsx")
library(ggplot2)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
In [2]:
bcc_all_metadata<-readRDS("/media/garret/New Volume/scRNAseq_data/Personalis/bcc_all_metadata.rds")
bcc_scRNA_counts<-readRDS("/media/garret/New Volume/scRNAseq_data/Personalis/bcc_scRNA_counts.rds")
bcc_tcell_metadata<-readRDS("/media/garret/New Volume/scRNAseq_data/Personalis/bcc_tcell_metadata.rds")
bcc_tcr<-readRDS("/media/garret/New Volume/scRNAseq_data/Personalis/bcc_tcr.rds")
In [3]:
dim(bcc_all_metadata)
dim(bcc_scRNA_counts)
dim(bcc_tcell_metadata)
dim(bcc_tcr)
- 53030
- 7
- 23309
- 53030
- 33106
- 6
- 28408
- 2
In [4]:
unique(bcc_all_metadata$treatment)
unique(bcc_all_metadata$patient)
- 'post'
- 'pre'
- 'su001'
- 'su002'
- 'su003'
- 'su004'
- 'su005'
- 'su006'
- 'su007'
- 'su008'
- 'su009'
- 'su010'
- 'su012'
Joint Clustering of 22 samples using Seurat V3¶
In [39]:
all<-CreateSeuratObject(counts = bcc_scRNA_counts, min.cells = 3, min.features = 200, project = "Yost")
Warning message:
“Feature names cannot have underscores ('_'), replacing with dashes ('-')”
In [40]:
mito.features <- grep(pattern = "^MT-", x = rownames(x = all), value = TRUE)
percent.mito <- Matrix::colSums(x = GetAssayData(object = all, slot = 'counts')[mito.features, ]) / Matrix::colSums(x = GetAssayData(object = all, slot = 'counts'))
all[['percent.mito']] <- percent.mito
In [15]:
#all<- subset(x = all, subset = nCount_RNA > 700 & nCount_RNA < 20000 & percent.mito < 0.10) # this time respect authors threshold
In [41]:
# subsettting data into individual samples
su001_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su001" & treatment=="pre")$cell.id)
su001_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su001" & treatment=="post")$cell.id)
su002_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su002" & treatment=="pre")$cell.id)
su002_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su002" & treatment=="post")$cell.id)
su003_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su003" & treatment=="pre")$cell.id)
su003_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su003" & treatment=="post")$cell.id)
su004_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su004" & treatment=="pre")$cell.id)
su004_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su004" & treatment=="post")$cell.id)
su005_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su005" & treatment=="pre")$cell.id)
su005_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su005" & treatment=="post")$cell.id)
su006_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su006" & treatment=="pre")$cell.id)
su006_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su006" & treatment=="post")$cell.id)
su007_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su007" & treatment=="pre")$cell.id)
su007_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su007" & treatment=="post")$cell.id)
su008_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su008" & treatment=="pre")$cell.id)
su008_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su008" & treatment=="post")$cell.id)
su009_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su009" & treatment=="pre")$cell.id)
su009_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su009" & treatment=="post")$cell.id)
su010_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su010" & treatment=="pre")$cell.id)
su010_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su010" & treatment=="post")$cell.id)
su012_pre<-subset(all,cells=subset(bcc_all_metadata,patient=="su012" & treatment=="pre")$cell.id)
su012_post<-subset(all,cells=subset(bcc_all_metadata,patient=="su012" & treatment=="post")$cell.id)
Integration(Log-normalize)¶
In [44]:
su001_pre<- NormalizeData(object = su001_pre,verbose = FALSE)
su001_post<- NormalizeData(object =su001_post,verbose = FALSE)
su002_pre<- NormalizeData(object = su002_pre,verbose = FALSE)
su002_post<- NormalizeData(object =su002_post,verbose = FALSE)
su003_pre<- NormalizeData(object = su003_pre,verbose = FALSE)
su003_post<- NormalizeData(object =su003_post,verbose = FALSE)
su004_pre<- NormalizeData(object = su004_pre,verbose = FALSE)
su004_post<- NormalizeData(object =su004_post,verbose = FALSE)
su005_pre<- NormalizeData(object = su005_pre,verbose = FALSE)
su005_post<- NormalizeData(object =su005_post,verbose = FALSE)
su006_pre<- NormalizeData(object = su006_pre,verbose = FALSE)
su006_post<- NormalizeData(object =su006_post,verbose = FALSE)
su007_pre<- NormalizeData(object = su007_pre,verbose = FALSE)
su007_post<- NormalizeData(object =su007_post,verbose = FALSE)
su008_pre<- NormalizeData(object = su008_pre,verbose = FALSE)
su008_post<- NormalizeData(object =su008_post,verbose = FALSE)
su009_pre<- NormalizeData(object = su009_pre,verbose = FALSE)
su009_post<- NormalizeData(object =su009_post,verbose = FALSE)
su010_pre<- NormalizeData(object = su010_pre,verbose = FALSE)
su010_post<- NormalizeData(object =su010_post,verbose = FALSE)
su012_pre<- NormalizeData(object = su012_pre,verbose = FALSE)
su012_post<- NormalizeData(object =su012_post,verbose = FALSE)
In [45]:
su001_pre<- FindVariableFeatures(object =su001_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su001_post<- FindVariableFeatures(object =su001_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su002_pre<- FindVariableFeatures(object =su002_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su002_post<- FindVariableFeatures(object =su002_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su003_pre<- FindVariableFeatures(object =su003_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su003_post<- FindVariableFeatures(object =su003_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su004_pre<- FindVariableFeatures(object =su004_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su004_post<- FindVariableFeatures(object =su004_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su005_pre<- FindVariableFeatures(object =su005_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su005_post<- FindVariableFeatures(object =su005_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su006_pre<- FindVariableFeatures(object =su006_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su006_post<- FindVariableFeatures(object =su006_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su007_pre<- FindVariableFeatures(object =su007_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su007_post<- FindVariableFeatures(object =su007_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su008_pre<- FindVariableFeatures(object =su008_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su008_post<- FindVariableFeatures(object =su008_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su009_pre<- FindVariableFeatures(object =su009_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su009_post<- FindVariableFeatures(object =su009_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su010_pre<- FindVariableFeatures(object =su010_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su010_post<- FindVariableFeatures(object =su010_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su012_pre<- FindVariableFeatures(object =su012_pre,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
su012_post<- FindVariableFeatures(object =su012_post,selection.method = "vst", nfeatures = 2000, verbose = FALSE)
In [46]:
su.list<-objects()
su.list$su001_pre<-su001_pre
su.list$su001_post<-su001_post
su.list$su002_pre<-su002_pre
su.list$su002_post<-su002_post
su.list$su003_pre<-su003_pre
su.list$su003_post<-su003_post
su.list$su004_pre<-su004_pre
su.list$su004_post<-su004_post
su.list$su005_pre<-su005_pre
su.list$su005_post<-su005_post
su.list$su006_pre<-su006_pre
su.list$su006_post<-su006_post
su.list$su007_pre<-su007_pre
su.list$su007_post<-su007_post
su.list$su008_pre<-su008_pre
su.list$su008_post<-su008_post
su.list$su009_pre<-su009_pre
su.list$su009_post<-su009_post
su.list$su010_pre<-su010_pre
su.list$su010_post<-su010_post
su.list$su012_pre<-su012_pre
su.list$su012_post<-su012_post
Warning message in su.list$su001_pre <- su001_pre: “Coercing LHS to a list”
In [47]:
reference.list <- su.list[c("su001_pre","su001_post","su002_pre","su002_post","su003_pre","su003_post","su004_pre","su004_post","su005_pre","su005_post","su006_pre","su006_post","su007_pre","su007_post","su008_pre","su008_post","su009_pre","su009_post","su010_pre","su010_post","su012_pre","su012_post")]
In [49]:
su.anchors <- FindIntegrationAnchors(object.list = reference.list, dims = 1:40,k.filter = 100)
Computing 2000 integration features Scaling features for provided objects Finding all pairwise anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 5085 anchors Filtering anchors Retained 1348 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 674 anchors Filtering anchors Retained 659 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 701 anchors Filtering anchors Retained 640 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1002 anchors Filtering anchors Retained 859 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1018 anchors Filtering anchors Retained 868 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 628 anchors Filtering anchors Retained 495 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 904 anchors Filtering anchors Retained 824 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1052 anchors Filtering anchors Retained 928 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 642 anchors Filtering anchors Retained 560 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 795 anchors Filtering anchors Retained 633 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2821 anchors Filtering anchors Retained 1029 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3745 anchors Filtering anchors Retained 1534 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 691 anchors Filtering anchors Retained 463 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 975 anchors Filtering anchors Retained 507 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1051 anchors Filtering anchors Retained 714 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2694 anchors Filtering anchors Retained 1783 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3305 anchors Filtering anchors Retained 2026 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 651 anchors Filtering anchors Retained 419 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 997 anchors Filtering anchors Retained 612 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 899 anchors Filtering anchors Retained 588 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2259 anchors Filtering anchors Retained 1105 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2181 anchors Filtering anchors Retained 1582 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3005 anchors Filtering anchors Retained 2130 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 715 anchors Filtering anchors Retained 500 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1007 anchors Filtering anchors Retained 565 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1044 anchors Filtering anchors Retained 775 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1891 anchors Filtering anchors Retained 1270 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1952 anchors Filtering anchors Retained 1420 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3850 anchors Filtering anchors Retained 1959 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7683 anchors Filtering anchors Retained 3090 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 715 anchors Filtering anchors Retained 321 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1008 anchors Filtering anchors Retained 429 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1103 anchors Filtering anchors Retained 645 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2827 anchors Filtering anchors Retained 1292 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2975 anchors Filtering anchors Retained 1416 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3208 anchors Filtering anchors Retained 2011 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4606 anchors Filtering anchors Retained 1914 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9590 anchors Filtering anchors Retained 4422 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 709 anchors Filtering anchors Retained 296 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1011 anchors Filtering anchors Retained 387 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1040 anchors Filtering anchors Retained 463 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3274 anchors Filtering anchors Retained 979 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3134 anchors Filtering anchors Retained 1272 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3106 anchors Filtering anchors Retained 1769 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6145 anchors Filtering anchors Retained 3799 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4646 anchors Filtering anchors Retained 1592 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 12070 anchors Filtering anchors Retained 3382 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 697 anchors Filtering anchors Retained 260 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1025 anchors Filtering anchors Retained 333 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1100 anchors Filtering anchors Retained 499 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3519 anchors Filtering anchors Retained 1447 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3161 anchors Filtering anchors Retained 973 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2972 anchors Filtering anchors Retained 1393 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6260 anchors Filtering anchors Retained 3088 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7810 anchors Filtering anchors Retained 3574 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4531 anchors Filtering anchors Retained 1470 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9642 anchors Filtering anchors Retained 3026 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 713 anchors Filtering anchors Retained 334 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1025 anchors Filtering anchors Retained 376 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1092 anchors Filtering anchors Retained 631 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3063 anchors Filtering anchors Retained 1250 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3060 anchors Filtering anchors Retained 1099 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2984 anchors Filtering anchors Retained 1597 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6245 anchors Filtering anchors Retained 3018 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7415 anchors Filtering anchors Retained 2689 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 8134 anchors Filtering anchors Retained 4780 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4104 anchors Filtering anchors Retained 1728 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7111 anchors Filtering anchors Retained 2539 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 684 anchors Filtering anchors Retained 348 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1023 anchors Filtering anchors Retained 470 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1031 anchors Filtering anchors Retained 750 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2821 anchors Filtering anchors Retained 1142 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2938 anchors Filtering anchors Retained 1243 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2585 anchors Filtering anchors Retained 1322 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4988 anchors Filtering anchors Retained 2495 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 5791 anchors Filtering anchors Retained 2350 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 5472 anchors Filtering anchors Retained 2763 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 5951 anchors Filtering anchors Retained 3075 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1169 anchors Filtering anchors Retained 980 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1217 anchors Filtering anchors Retained 933 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 637 anchors Filtering anchors Retained 495 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 840 anchors Filtering anchors Retained 655 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 832 anchors Filtering anchors Retained 654 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1105 anchors Filtering anchors Retained 805 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1183 anchors Filtering anchors Retained 932 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1194 anchors Filtering anchors Retained 961 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1224 anchors Filtering anchors Retained 1043 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1225 anchors Filtering anchors Retained 977 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1227 anchors Filtering anchors Retained 1024 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1211 anchors Filtering anchors Retained 966 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1185 anchors Filtering anchors Retained 1020 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3911 anchors Filtering anchors Retained 1830 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 8122 anchors Filtering anchors Retained 3157 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 703 anchors Filtering anchors Retained 389 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1011 anchors Filtering anchors Retained 412 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1092 anchors Filtering anchors Retained 705 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3234 anchors Filtering anchors Retained 1404 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2958 anchors Filtering anchors Retained 1340 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2745 anchors Filtering anchors Retained 1679 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 5271 anchors Filtering anchors Retained 3308 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6010 anchors Filtering anchors Retained 2824 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6968 anchors Filtering anchors Retained 3451 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6072 anchors Filtering anchors Retained 3043 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4788 anchors Filtering anchors Retained 2113 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1222 anchors Filtering anchors Retained 478 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4928 anchors Filtering anchors Retained 1276 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 13434 anchors Filtering anchors Retained 3805 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 695 anchors Filtering anchors Retained 246 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1019 anchors Filtering anchors Retained 319 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1035 anchors Filtering anchors Retained 486 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3539 anchors Filtering anchors Retained 824 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3265 anchors Filtering anchors Retained 1034 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2813 anchors Filtering anchors Retained 1194 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6542 anchors Filtering anchors Retained 2344 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 8883 anchors Filtering anchors Retained 2511 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9070 anchors Filtering anchors Retained 2589 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9057 anchors Filtering anchors Retained 2121 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6898 anchors Filtering anchors Retained 1847 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1221 anchors Filtering anchors Retained 390 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6654 anchors Filtering anchors Retained 2792 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 5000 anchors Filtering anchors Retained 1375 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 14288 anchors Filtering anchors Retained 3135 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 715 anchors Filtering anchors Retained 154 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1021 anchors Filtering anchors Retained 262 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1165 anchors Filtering anchors Retained 240 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3743 anchors Filtering anchors Retained 637 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3312 anchors Filtering anchors Retained 842 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3599 anchors Filtering anchors Retained 719 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7945 anchors Filtering anchors Retained 1875 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9359 anchors Filtering anchors Retained 2020 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 11180 anchors Filtering anchors Retained 2222 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 10216 anchors Filtering anchors Retained 1755 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6846 anchors Filtering anchors Retained 1626 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1242 anchors Filtering anchors Retained 299 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7572 anchors Filtering anchors Retained 1921 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 11207 anchors Filtering anchors Retained 2800 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4998 anchors Filtering anchors Retained 1346 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 16082 anchors Filtering anchors Retained 3477 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 698 anchors Filtering anchors Retained 147 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1020 anchors Filtering anchors Retained 303 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1133 anchors Filtering anchors Retained 227 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3674 anchors Filtering anchors Retained 536 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3240 anchors Filtering anchors Retained 797 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3547 anchors Filtering anchors Retained 786 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 8304 anchors Filtering anchors Retained 1693 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9979 anchors Filtering anchors Retained 2369 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 11835 anchors Filtering anchors Retained 2197 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 10358 anchors Filtering anchors Retained 1519 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6994 anchors Filtering anchors Retained 1463 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1216 anchors Filtering anchors Retained 315 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7600 anchors Filtering anchors Retained 1992 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 12144 anchors Filtering anchors Retained 2719 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 11365 anchors Filtering anchors Retained 6058 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 532 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 527 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 493 anchors Filtering anchors Retained 479 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 527 anchors Filtering anchors Retained 512 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 530 anchors Filtering anchors Retained 508 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 539 anchors Filtering anchors Retained 527 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 526 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 535 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 530 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 517 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 532 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 526 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 534 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 534 anchors Filtering anchors Retained 529 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 525 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 536 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 533 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 528 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2330 anchors Filtering anchors Retained 1372 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2599 anchors Filtering anchors Retained 1440 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 700 anchors Filtering anchors Retained 357 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 991 anchors Filtering anchors Retained 568 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1067 anchors Filtering anchors Retained 524 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2149 anchors Filtering anchors Retained 934 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2118 anchors Filtering anchors Retained 1183 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2117 anchors Filtering anchors Retained 1086 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2505 anchors Filtering anchors Retained 1493 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2554 anchors Filtering anchors Retained 1514 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2602 anchors Filtering anchors Retained 1454 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2574 anchors Filtering anchors Retained 1258 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2433 anchors Filtering anchors Retained 1333 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1164 anchors Filtering anchors Retained 612 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2486 anchors Filtering anchors Retained 1623 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2571 anchors Filtering anchors Retained 1549 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2577 anchors Filtering anchors Retained 1753 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2607 anchors Filtering anchors Retained 1844 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 539 anchors Filtering anchors Retained 323 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 4658 anchors Filtering anchors Retained 1622 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 10603 anchors Filtering anchors Retained 3196 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 705 anchors Filtering anchors Retained 204 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1001 anchors Filtering anchors Retained 375 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1128 anchors Filtering anchors Retained 317 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3620 anchors Filtering anchors Retained 812 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3180 anchors Filtering anchors Retained 1038 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3320 anchors Filtering anchors Retained 906 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6568 anchors Filtering anchors Retained 2124 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7886 anchors Filtering anchors Retained 2835 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 8096 anchors Filtering anchors Retained 2785 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 7439 anchors Filtering anchors Retained 1980 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 5969 anchors Filtering anchors Retained 1698 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1214 anchors Filtering anchors Retained 405 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 6729 anchors Filtering anchors Retained 2132 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9417 anchors Filtering anchors Retained 1938 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9235 anchors Filtering anchors Retained 2756 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 9680 anchors Filtering anchors Retained 3050 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 180 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2567 anchors Filtering anchors Retained 795 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3083 anchors Filtering anchors Retained 1493 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3822 anchors Filtering anchors Retained 1747 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 703 anchors Filtering anchors Retained 291 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 998 anchors Filtering anchors Retained 518 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1131 anchors Filtering anchors Retained 418 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2662 anchors Filtering anchors Retained 1054 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2580 anchors Filtering anchors Retained 1237 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2673 anchors Filtering anchors Retained 1158 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3564 anchors Filtering anchors Retained 1611 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3647 anchors Filtering anchors Retained 1868 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3658 anchors Filtering anchors Retained 1918 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3631 anchors Filtering anchors Retained 1802 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3382 anchors Filtering anchors Retained 1542 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 1205 anchors Filtering anchors Retained 580 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3538 anchors Filtering anchors Retained 1680 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3779 anchors Filtering anchors Retained 1431 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3757 anchors Filtering anchors Retained 1646 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3812 anchors Filtering anchors Retained 1811 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 540 anchors Filtering anchors Retained 233 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 2236 anchors Filtering anchors Retained 1044 anchors Running CCA Merging objects Finding neighborhoods Finding anchors Found 3540 anchors Filtering anchors Retained 2276 anchors
In [50]:
bcc.integrated <- IntegrateData(anchorset = su.anchors, dims = 1:40)
Merging dataset 19 into 16 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 3 into 1 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 4 into 2 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 14 into 9 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 5 into 1 3 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 20 into 18 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 22 into 21 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 7 into 2 4 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 8 into 9 14 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 6 into 11 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 1 3 5 into 9 14 8 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 13 into 12 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 17 into 18 20 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 10 into 9 14 8 1 3 5 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 15 into 11 6 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 21 22 into 2 4 7 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 12 13 into 11 6 15 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 9 14 8 1 3 5 10 into 2 4 7 21 22 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 16 19 into 2 4 7 21 22 9 14 8 1 3 5 10 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 18 20 17 into 2 4 7 21 22 9 14 8 1 3 5 10 16 19 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Merging dataset 11 6 15 12 13 into 2 4 7 21 22 9 14 8 1 3 5 10 16 19 18 20 17 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights Integrating data Warning message: “Adding a command log without an assay associated with it”
In [51]:
library(cowplot)
# switch to integrated assay. The variable features of this assay are
# automatically set during IntegrateData
DefaultAssay(object = bcc.integrated) <- "integrated"
# Run the standard workflow for visualization and clustering
bcc.integrated <- ScaleData(object = bcc.integrated, verbose = FALSE)
bcc.integrated <- RunPCA(object = bcc.integrated, npcs = 40, verbose = FALSE)
bcc.integrated <- RunUMAP(object = bcc.integrated, reduction = "pca",
dims = 1:40)
Warning message: “The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation' This message will be shown once per session” 23:13:15 UMAP embedding parameters a = 0.9922 b = 1.112 23:13:15 Read 53029 rows and found 40 numeric columns 23:13:15 Using Annoy for neighbor search, n_neighbors = 30 23:13:15 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * | 23:13:21 Writing NN index file to temp file /tmp/RtmppibU3g/file24f0696f0c54 23:13:21 Searching Annoy index using 1 thread, search_k = 3000 23:13:36 Annoy recall = 100% 23:13:36 Commencing smooth kNN distance calibration using 1 thread 23:13:38 Initializing from normalized Laplacian + noise 23:13:40 Commencing optimization for 200 epochs, with 2660696 positive edges 23:14:01 Optimization finished
In [64]:
stim<-numeric()
for(i in 1:dim(bcc.integrated@meta.data)[1]){
temp<-subset(bcc_all_metadata,cell.id==rownames(bcc.integrated@meta.data)[i])
stim<-c(stim,paste(temp$patient,"_",temp$treatment,sep=""))
}
bcc.integrated@meta.data$stim<-stim
In [68]:
treatment<-numeric()
for(i in 1:dim(bcc.integrated@meta.data)[1]){
temp<-subset(bcc_all_metadata,cell.id==rownames(bcc.integrated@meta.data)[i])
treatment<-c(treatment,temp$treatment)
}
bcc.integrated@meta.data$treatment<-treatment
In [69]:
patient<-numeric()
for(i in 1:dim(bcc.integrated@meta.data)[1]){
temp<-subset(bcc_all_metadata,cell.id==rownames(bcc.integrated@meta.data)[i])
patient<-c(patient,temp$patient)
}
bcc.integrated@meta.data$patient<-patient
In [123]:
sort<-numeric()
for(i in 1:dim(bcc.integrated@meta.data)[1]){
temp<-subset(bcc_all_metadata,cell.id==rownames(bcc.integrated@meta.data)[i])
sort<-c(sort,temp$sort)
}
bcc.integrated@meta.data$sort<-sort
In [127]:
original_cluster<-numeric()
for(i in 1:dim(bcc.integrated@meta.data)[1]){
temp<-subset(bcc_all_metadata,cell.id==rownames(bcc.integrated@meta.data)[i])
original_cluster<-c(original_cluster,temp$cluster)
}
bcc.integrated@meta.data$original_cluster<-original_cluster
In [70]:
p1 <- DimPlot(object = bcc.integrated, reduction = "umap", group.by = "stim", label = TRUE, repel = TRUE)
plot_grid(p1,label_size = 30)
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/all_cell_umap_stim.pdf",width=10,height=10)
Warning message: “ggrepel: 14 unlabeled data points (too many overlaps). Consider increasing max.overlaps” Warning message: “ggrepel: 13 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
In [71]:
p1 <- DimPlot(object = bcc.integrated, reduction = "umap", group.by = "treatment", label = TRUE, repel = TRUE)
plot_grid(p1,label_size = 30)
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/all_cell_umap_treatment.pdf",width=10,height=10)
In [72]:
p1 <- DimPlot(object = bcc.integrated, reduction = "umap", group.by = "patient", label = TRUE, repel = TRUE)
plot_grid(p1,label_size = 30)
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/all_cell_umap_patient.pdf",width=10,height=10)
Warning message: “ggrepel: 5 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
In [124]:
p1 <- DimPlot(object = bcc.integrated, reduction = "umap", group.by = "sort", label = TRUE, repel = TRUE)
plot_grid(p1,label_size = 30)
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/all_cell_umap_sort.pdf",width=10,height=10)
integrated analysis¶
In [81]:
#used default setting
DefaultAssay(object = bcc.integrated) <- "integrated"
bcc.integrated <- FindNeighbors(object = bcc.integrated)
bcc.integrated <- FindClusters(bcc.integrated, resolution = 0.6)
Computing nearest neighbor graph Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 53029 Number of edges: 1773632 Running Louvain algorithm... Maximum modularity in 10 random starts: 0.9183 Number of communities: 21 Elapsed time: 10 seconds
In [56]:
library(ggplot2)
In [82]:
DimPlot(object = bcc.integrated, reduction = "umap", group.by = "integrated_snn_res.0.6", label = TRUE, repel = TRUE)
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/allcell_umap_number_0.6.pdf",width=10,height=10)
In [83]:
# this is important
DefaultAssay(bcc.integrated) <- "RNA"
In [125]:
saveRDS(bcc.integrated, file = "/media/garret/New Volume/scRNAseq_data/Personalis/bcc.integrated.rds")
Visualizing gene expression in UMAP space¶
In [101]:
#T cells
FeaturePlot(object =bcc.integrated, features = c("CD3G","CD3D","CD3E","CD2"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_CD3G_CD3D_CD3E_CD2.pdf",width=10,height=10)
In [102]:
#CD8 T cells
FeaturePlot(object =bcc.integrated, features = c("CD8A","GZMA"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_CD8A_GZMA.pdf",width=10,height=10)
In [118]:
#CD8 T cells
FeaturePlot(object =bcc.integrated, features = c("CD45","CD3"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_CD45_CD3.pdf",width=10,height=10)
Warning message in FetchData(object = object, vars = c(dims, "ident", features), : “The following requested variables were not found: CD45, CD3”
Error: None of the requested features were found: CD45, CD3 in slot data
Traceback:
1. FeaturePlot(object = bcc.integrated, features = c("CD45", "CD3"),
. cols = c("lightgrey", "blue"))
2. stop("None of the requested features were found: ", paste(features,
. collapse = ", "), " in slot ", slot, call. = FALSE)
In [103]:
#CD4 T cells
FeaturePlot(object =bcc.integrated, features = c("CD4","FOXP3"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_CD4_FOXP3.pdf",width=10,height=10)
In [104]:
#NKcells
FeaturePlot(object =bcc.integrated, features = c("KLRC1","KLRC3"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_KLRC1_KLRC3.pdf",width=10,height=10)
In [105]:
#B cells
FeaturePlot(object =bcc.integrated, features = c("CD19","CD79A"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_CD19_CD79A.pdf",width=10,height=10)
In [106]:
#plasma cells
FeaturePlot(object =bcc.integrated, features = c("SLAMF7","IGKC"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_SLAMF7_IGKC.pdf",width=10,height=10)
In [107]:
#macrophages
FeaturePlot(object =bcc.integrated, features = c("FCGR2A","CSF1R"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_FCGR2A_CSF1R.pdf",width=10,height=10)
In [108]:
#dendtiric cells
FeaturePlot(object =bcc.integrated, features = c("FLT3"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_FLT3.pdf",width=10,height=10)
In [109]:
#plasmacytoid dendritic cells
FeaturePlot(object =bcc.integrated, features = c("CLEC4C"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_CLE4C.pdf",width=10,height=10)
In [110]:
#fibroblasts
FeaturePlot(object =bcc.integrated, features = c("COL1A2"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_COL1A2.pdf",width=10,height=10)
In [111]:
#myofibroblasts
FeaturePlot(object =bcc.integrated, features = c("MCAM","MYLK"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_MCAM_MYLK.pdf",width=10,height=10)
In [112]:
#cancer-associated fibroblast
FeaturePlot(object =bcc.integrated, features = c("FAP","PDPN"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_FAP_PDPN.pdf",width=10,height=10)
In [113]:
#malignast cells
FeaturePlot(object =bcc.integrated, features = c("EPCAM","TP63"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_EPCAM_TP63.pdf",width=10,height=10)
In [114]:
#endothelial cells
FeaturePlot(object =bcc.integrated, features = c("PECAM1","VWF"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_PECAM1_VWF.pdf",width=10,height=10)
In [115]:
#melanocytes
FeaturePlot(object =bcc.integrated, features = c("PMEL","MLANA"), cols = c("lightgrey", "blue"))
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/bcc_UMAP_feature_PMEL_MLANA.pdf",width=10,height=10)
Upload seurat object. You can start from here¶
In [3]:
# res 0.6
bcc.integrated<-readRDS(file = "/media/garret/New Volume/scRNAseq_data/Personalis/bcc.integrated.rds")
# this is important
DefaultAssay(bcc.integrated) <- "RNA"
assgin clusters to cell types¶
In [4]:
new.ident <- c("Bcell","CD4_Tcell1","CD8_Tcell1","CD8_Tcell2","CD4_Tcell2",
"CD4_Tcell3","Malignant_cell","Plasma_cell","CD4_Tcell4","NK_cell",
"CD4_Tcell5","Dendritic_cell","CD8_Tcell3","Macrophage","CD8_Tcell4",
"CD8_Tcell5","CD8_Tcell6","Fibroblast","Plasmacytoid_dendritic_cell","Endotherial_cell",
"Myofibroblast")
names(x = new.ident) <- levels(x =bcc.integrated)
bcc.integrated<- RenameIdents(object =bcc.integrated, new.ident)
In [133]:
DimPlot(object = bcc.integrated, reduction = "umap", label.size =4, label = TRUE, repel = TRUE)
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/allcell_umap_name.pdf",width=15,height=10)
In [131]:
# comparision with my original cluster
p1 <- DimPlot(object = bcc.integrated, reduction = "umap", group.by = "original_cluster", label = TRUE, repel = TRUE)
plot_grid(p1,label_size = 30)
ggsave(file="/media/garret/New Volume/scRNAseq_data/Personalis/all_cell_umap_original_cluster.pdf",width=10,height=10)
In [5]:
for (i in 1:length(new.ident)){
assign(paste(new.ident[i],"_barcode",sep=""),colnames(bcc.integrated@assays$RNA@data[,which(Idents(object=bcc.integrated) %in% new.ident[i])]))# this gives all barcodes in cluster
}
In [135]:
T_barcode<-c(CD4_Tcell1_barcode,CD4_Tcell2_barcode,CD4_Tcell3_barcode,CD4_Tcell4_barcode,CD4_Tcell5_barcode,CD8_Tcell1_barcode,CD8_Tcell2_barcode,CD8_Tcell3_barcode,CD8_Tcell4_barcode,CD8_Tcell5_barcode)
In [136]:
saveRDS(T_barcode, file = "/media/garret/New Volume/scRNAseq_data/Personalis/T_id.rds")
conserved markers for clusters¶
In [6]:
DefaultAssay(bcc.integrated) <- "integrated"
In [7]:
for (i in 1:length(new.ident)){
one.markers <- FindConservedMarkers(bcc.integrated, ident.1 = new.ident[i], grouping.var = "stim",print.bar = FALSE, min.cells.feature = 1,min.cells.group = 1)
write.xlsx2(one.markers,file=(paste("/media/garret/New Volume/scRNAseq_data/Personalis/Marker/",new.ident[i],"_gene.xlsx",sep="")))}
Warning message: “Identity: Bcell not present in group su010_pre. Skipping su010_pre” Warning message: “Identity: Bcell not present in group su002_pre. Skipping su002_pre” Testing group su002_post: (Bcell) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Warning message: “Identity: Bcell not present in group su003_pre. Skipping su003_pre” Testing group su007_post: (Bcell) vs (Dendritic_cell, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Warning message: “Identity: Bcell not present in group su010_post. Skipping su010_post” Testing group su004_pre: (Bcell) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (Bcell) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (Bcell) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (Bcell) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Bcell) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5) Testing group su007_pre: (Bcell) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell) Testing group su008_pre: (Bcell) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (Bcell) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (Bcell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (Bcell) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (Bcell) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (Bcell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Myofibroblast) Testing group su009_post: (Bcell) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (Bcell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (Bcell) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (Bcell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD4_Tcell1) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD4_Tcell1) vs (Macrophage, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD4_Tcell1) vs (CD8_Tcell4, CD4_Tcell2, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD4_Tcell1) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD4_Tcell1) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD4_Tcell1) vs (CD4_Tcell2, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD4_Tcell1) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD4_Tcell1) vs (CD8_Tcell4, CD8_Tcell5, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD4_Tcell1) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD4_Tcell1) vs (Malignant_cell, Dendritic_cell, Fibroblast, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD4_Tcell1) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD4_Tcell1) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD4_Tcell1) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD4_Tcell1) vs (Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD4_Tcell1) vs (Macrophage, CD8_Tcell5, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD4_Tcell1) vs (CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD4_Tcell1) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD4_Tcell1) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD4_Tcell1) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD4_Tcell1) vs (CD8_Tcell2, CD4_Tcell3, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD4_Tcell1) vs (Plasma_cell, Macrophage, CD8_Tcell5, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD4_Tcell1) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Warning message: “Identity: CD8_Tcell1 not present in group su010_pre. Skipping su010_pre” Testing group su002_pre: (CD8_Tcell1) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD8_Tcell1) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD8_Tcell1) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD8_Tcell1) vs (Dendritic_cell, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD8_Tcell1) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD8_Tcell1) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD8_Tcell1) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD8_Tcell1) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD8_Tcell1) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD8_Tcell1) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD8_Tcell1) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD8_Tcell1) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD8_Tcell1) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD8_Tcell1) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD8_Tcell1) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD8_Tcell1) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD8_Tcell1) vs (CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD8_Tcell1) vs (CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD8_Tcell1) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD8_Tcell1) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD8_Tcell1) vs (CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD8_Tcell2) vs (CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD8_Tcell2) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD8_Tcell2) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD8_Tcell2) vs (CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD8_Tcell2) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD8_Tcell2) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD8_Tcell2) vs (CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD8_Tcell2) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD8_Tcell2) vs (CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD8_Tcell2) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD8_Tcell2) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD8_Tcell2) vs (CD4_Tcell1, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD8_Tcell2) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD8_Tcell2) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD8_Tcell2) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD8_Tcell2) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD8_Tcell2) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD8_Tcell2) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD8_Tcell2) vs (CD8_Tcell1, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD8_Tcell2) vs (CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD8_Tcell2) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD8_Tcell2) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD4_Tcell2) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD4_Tcell2) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD4_Tcell2) vs (CD8_Tcell4, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD4_Tcell2) vs (CD8_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD4_Tcell2) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD4_Tcell2) vs (CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD4_Tcell2) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD4_Tcell2) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD4_Tcell2) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD4_Tcell2) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD4_Tcell2) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD4_Tcell2) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD4_Tcell2) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD4_Tcell2) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD4_Tcell2) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD4_Tcell2) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD4_Tcell2) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD4_Tcell2) vs (CD8_Tcell1, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD4_Tcell2) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD4_Tcell2) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD4_Tcell2) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD4_Tcell2) vs (CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD4_Tcell3) vs (CD8_Tcell2, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD4_Tcell3) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD4_Tcell3) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD4_Tcell3) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD4_Tcell3) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD4_Tcell3) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD4_Tcell3) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD4_Tcell3) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD4_Tcell3) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD4_Tcell3) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD4_Tcell3) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD4_Tcell3) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD4_Tcell3) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD4_Tcell3) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD4_Tcell3) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD4_Tcell3) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD4_Tcell3) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD4_Tcell3) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD4_Tcell3) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD4_Tcell3) vs (CD8_Tcell2, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD4_Tcell3) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD4_Tcell3) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (Malignant_cell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (Malignant_cell) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Warning message: “Identity: Malignant_cell not present in group su002_post. Skipping su002_post” Testing group su003_pre: (Malignant_cell) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (Malignant_cell) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (Malignant_cell) vs (CD4_Tcell2, CD4_Tcell1, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (Malignant_cell) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (Malignant_cell) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (Malignant_cell) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (Malignant_cell) vs (Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Malignant_cell) vs (CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (Malignant_cell) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (Malignant_cell) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (Malignant_cell) vs (CD4_Tcell1, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (Malignant_cell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (Malignant_cell) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell) Testing group su006_post: (Malignant_cell) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Myofibroblast, Endotherial_cell) Testing group su009_pre: (Malignant_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (Malignant_cell) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (Malignant_cell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (Malignant_cell) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su001_post: (Malignant_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5) Testing group su010_pre: (Plasma_cell) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (Plasma_cell) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (Plasma_cell) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (Plasma_cell) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (Plasma_cell) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (Plasma_cell) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasmacytoid_dendritic_cell) Testing group su004_pre: (Plasma_cell) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su012_post: (Plasma_cell) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (Plasma_cell) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Endotherial_cell) Testing group su003_post: (Plasma_cell) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5) Testing group su001_pre: (Plasma_cell) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (Plasma_cell) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (Plasma_cell) vs (Plasmacytoid_dendritic_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (Plasma_cell) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (Plasma_cell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (Plasma_cell) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (Plasma_cell) vs (Macrophage, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (Plasma_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Bcell, Myofibroblast) Testing group su009_post: (Plasma_cell) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (Plasma_cell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (Plasma_cell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (Plasma_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Warning message: “Identity: CD4_Tcell4 not present in group su010_pre. Skipping su010_pre” Testing group su002_pre: (CD4_Tcell4) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD4_Tcell4) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD4_Tcell4) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD4_Tcell4) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD4_Tcell4) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD4_Tcell4) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD4_Tcell4) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD4_Tcell4) vs (CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD4_Tcell4) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD4_Tcell4) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD4_Tcell4) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD4_Tcell4) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, Endotherial_cell) Testing group su012_pre: (CD4_Tcell4) vs (CD4_Tcell1, Malignant_cell, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD4_Tcell4) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD4_Tcell4) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD4_Tcell4) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD4_Tcell4) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD4_Tcell4) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD4_Tcell4) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD4_Tcell4) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD4_Tcell4) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (NK_cell) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (NK_cell) vs (Macrophage, CD4_Tcell1, Dendritic_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (NK_cell) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (NK_cell) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (NK_cell) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (NK_cell) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (NK_cell) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (NK_cell) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (NK_cell) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (NK_cell) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (NK_cell) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (NK_cell) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (NK_cell) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (NK_cell) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (NK_cell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (NK_cell) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (NK_cell) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (NK_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (NK_cell) vs (CD8_Tcell1, CD8_Tcell2, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (NK_cell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (NK_cell) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (NK_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD4_Tcell5) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD4_Tcell5) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD4_Tcell5) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD4_Tcell5) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD8_Tcell5) Testing group su007_post: (CD4_Tcell5) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD4_Tcell5) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD4_Tcell5) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD4_Tcell5) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD4_Tcell5) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD4_Tcell5) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, Plasma_cell) Testing group su001_pre: (CD4_Tcell5) vs (Malignant_cell, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD4_Tcell5) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD4_Tcell5) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD4_Tcell5) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD4_Tcell5) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD4_Tcell5) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD4_Tcell5) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD4_Tcell5) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD4_Tcell5) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD4_Tcell5) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD4_Tcell5) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD4_Tcell5) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (Dendritic_cell) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, CD8_Tcell6, Macrophage) Testing group su002_pre: (Dendritic_cell) vs (Macrophage, CD4_Tcell1, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (Dendritic_cell) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (Dendritic_cell) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (Dendritic_cell) vs (CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (Dendritic_cell) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (Dendritic_cell) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (Dendritic_cell) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell) Testing group su004_post: (Dendritic_cell) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (Dendritic_cell) vs (Malignant_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Dendritic_cell) vs (Malignant_cell, CD4_Tcell5, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (Dendritic_cell) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (Dendritic_cell) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (Dendritic_cell) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Plasmacytoid_dendritic_cell) Testing group su005_pre: (Dendritic_cell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (Dendritic_cell) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (Dendritic_cell) vs (Macrophage, Plasma_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (Dendritic_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (Dendritic_cell) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (Dendritic_cell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (Dendritic_cell) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (Dendritic_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD8_Tcell3) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD8_Tcell3) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD8_Tcell3) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD8_Tcell3) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD8_Tcell3) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD8_Tcell3) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD8_Tcell3) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD8_Tcell3) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD8_Tcell3) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD8_Tcell3) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD8_Tcell3) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD8_Tcell3) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD8_Tcell3) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD8_Tcell3) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD8_Tcell3) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD8_Tcell3) vs (CD4_Tcell1, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD8_Tcell3) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD8_Tcell3) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD8_Tcell3) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD8_Tcell3) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD8_Tcell3) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD8_Tcell3) vs (CD8_Tcell1, CD4_Tcell2, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (Macrophage) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6) Testing group su002_pre: (Macrophage) vs (CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (Macrophage) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (Macrophage) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (Macrophage) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Fibroblast, CD8_Tcell5) Testing group su010_post: (Macrophage) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (Macrophage) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (Macrophage) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (Macrophage) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (Macrophage) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Macrophage) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (Macrophage) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (Macrophage) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (Macrophage) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (Macrophage) vs (CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (Macrophage) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (Macrophage) vs (Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (Macrophage) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (Macrophage) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (Macrophage) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (Macrophage) vs (Plasma_cell, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (Macrophage) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD8_Tcell4) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD8_Tcell4) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD8_Tcell4) vs (CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD8_Tcell4) vs (CD8_Tcell2, CD4_Tcell2, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD8_Tcell4) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD8_Tcell4) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD8_Tcell4) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD8_Tcell4) vs (CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD8_Tcell4) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD8_Tcell4) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD8_Tcell4) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD8_Tcell4) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD8_Tcell4) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD8_Tcell4) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD8_Tcell4) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD8_Tcell4) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD8_Tcell4) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD8_Tcell4) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD8_Tcell4) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD8_Tcell4) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD8_Tcell4) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD8_Tcell4) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (CD8_Tcell5) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (CD8_Tcell5) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, Endotherial_cell) Warning message: “Identity: CD8_Tcell5 not present in group su002_post. Skipping su002_post” Testing group su003_pre: (CD8_Tcell5) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5) Testing group su007_post: (CD8_Tcell5) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast) Testing group su010_post: (CD8_Tcell5) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Warning message: “Identity: CD8_Tcell5 not present in group su004_pre. Skipping su004_pre” Testing group su012_post: (CD8_Tcell5) vs (CD8_Tcell4, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD8_Tcell5) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD8_Tcell5) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD8_Tcell5) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, Bcell) Testing group su007_pre: (CD8_Tcell5) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD8_Tcell5) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD8_Tcell5) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD8_Tcell5) vs (Macrophage, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD8_Tcell5) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD8_Tcell5) vs (Macrophage, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD8_Tcell5) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD8_Tcell5) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD8_Tcell5) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD8_Tcell5) vs (Plasma_cell, Macrophage, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD8_Tcell5) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, Malignant_cell) Warning message in max(nchar(aux)): “no non-missing arguments to max; returning -Inf” Testing group su010_pre: (CD8_Tcell6) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, Fibroblast, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, Macrophage) Testing group su002_pre: (CD8_Tcell6) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (CD8_Tcell6) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (CD8_Tcell6) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (CD8_Tcell6) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Testing group su010_post: (CD8_Tcell6) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (CD8_Tcell6) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (CD8_Tcell6) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (CD8_Tcell6) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (CD8_Tcell6) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (CD8_Tcell6) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (CD8_Tcell6) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (CD8_Tcell6) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (CD8_Tcell6) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (CD8_Tcell6) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (CD8_Tcell6) vs (CD4_Tcell1, CD8_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (CD8_Tcell6) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (CD8_Tcell6) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (CD8_Tcell6) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (CD8_Tcell6) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (CD8_Tcell6) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (CD8_Tcell6) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Testing group su010_pre: (Fibroblast) vs (CD8_Tcell2, CD4_Tcell3, Malignant_cell, CD4_Tcell1, NK_cell, CD4_Tcell5, CD4_Tcell2, CD8_Tcell5, Plasma_cell, CD8_Tcell3, CD8_Tcell4, Dendritic_cell, CD8_Tcell6, Macrophage) Testing group su002_pre: (Fibroblast) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (Fibroblast) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (Fibroblast) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (Fibroblast) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, CD8_Tcell5) Testing group su010_post: (Fibroblast) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell, Plasmacytoid_dendritic_cell) Testing group su004_pre: (Fibroblast) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (Fibroblast) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Plasma_cell, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell) Testing group su004_post: (Fibroblast) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (Fibroblast) vs (Malignant_cell, Dendritic_cell, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Fibroblast) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (Fibroblast) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (Fibroblast) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (Fibroblast) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell, Plasmacytoid_dendritic_cell) Testing group su005_pre: (Fibroblast) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (Fibroblast) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (Fibroblast) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (Fibroblast) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (Fibroblast) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell, Myofibroblast) Testing group su008_post: (Fibroblast) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (Fibroblast) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (Fibroblast) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Warning message: “Identity: Plasmacytoid_dendritic_cell not present in group su010_pre. Skipping su010_pre” Warning message: “Identity: Plasmacytoid_dendritic_cell not present in group su002_pre. Skipping su002_pre” Testing group su002_post: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Myofibroblast) Testing group su003_pre: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Warning message: “Identity: Plasmacytoid_dendritic_cell not present in group su007_post. Skipping su007_post” Testing group su010_post: (Plasmacytoid_dendritic_cell) vs (CD4_Tcell2, CD4_Tcell1, Malignant_cell, CD8_Tcell5, CD8_Tcell2, CD8_Tcell3, Macrophage, CD4_Tcell5, CD4_Tcell4, CD8_Tcell1, NK_cell, Dendritic_cell, Fibroblast, CD4_Tcell3, CD8_Tcell6, CD8_Tcell4, Plasma_cell) Testing group su004_pre: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Myofibroblast, Plasma_cell) Testing group su012_post: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell4, CD8_Tcell5, CD4_Tcell1, CD8_Tcell1, CD8_Tcell6, CD4_Tcell2, CD4_Tcell4, CD8_Tcell2, Macrophage, Malignant_cell, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Bcell, Fibroblast, Plasma_cell, NK_cell, Dendritic_cell) Testing group su004_post: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Malignant_cell, Bcell, Myofibroblast, Plasma_cell, Endotherial_cell) Testing group su003_post: (Plasmacytoid_dendritic_cell) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Plasmacytoid_dendritic_cell) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (Plasmacytoid_dendritic_cell) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Fibroblast, Myofibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (Plasmacytoid_dendritic_cell) vs (Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Testing group su012_pre: (Plasmacytoid_dendritic_cell) vs (CD4_Tcell1, Malignant_cell, CD4_Tcell4, Macrophage, CD4_Tcell3, CD8_Tcell4, CD8_Tcell1, CD4_Tcell5, NK_cell, Bcell, CD4_Tcell2, Plasma_cell, CD8_Tcell5, Fibroblast, CD8_Tcell2, CD8_Tcell3, CD8_Tcell6, Dendritic_cell) Testing group su005_pre: (Plasmacytoid_dendritic_cell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell, Myofibroblast) Testing group su005_post: (Plasmacytoid_dendritic_cell) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Myofibroblast, Endotherial_cell, Malignant_cell) Testing group su006_post: (Plasmacytoid_dendritic_cell) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast, Endotherial_cell) Testing group su009_pre: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Macrophage, Plasma_cell, Bcell, Myofibroblast) Testing group su009_post: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Myofibroblast) Testing group su008_post: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Bcell, Endotherial_cell, Myofibroblast) Testing group su006_pre: (Plasmacytoid_dendritic_cell) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell, Myofibroblast) Testing group su001_post: (Plasmacytoid_dendritic_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, Myofibroblast, CD8_Tcell5, Malignant_cell) Warning message: “Identity: Endotherial_cell not present in group su010_pre. Skipping su010_pre” Testing group su002_pre: (Endotherial_cell) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Myofibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5) Testing group su002_post: (Endotherial_cell) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Macrophage, Myofibroblast, Plasmacytoid_dendritic_cell) Testing group su003_pre: (Endotherial_cell) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, Myofibroblast, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (Endotherial_cell) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Myofibroblast, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Warning message: “Identity: Endotherial_cell not present in group su010_post. Skipping su010_post” Testing group su004_pre: (Endotherial_cell) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Malignant_cell, Plasmacytoid_dendritic_cell, Myofibroblast, Plasma_cell) Warning message: “Identity: Endotherial_cell not present in group su012_post. Skipping su012_post” Testing group su004_post: (Endotherial_cell) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Myofibroblast, Plasma_cell) Testing group su003_post: (Endotherial_cell) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Myofibroblast, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Endotherial_cell) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, Myofibroblast, CD8_Tcell5, Bcell) Testing group su007_pre: (Endotherial_cell) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Myofibroblast, Bcell) Testing group su008_pre: (Endotherial_cell) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, Myofibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4) Warning message: “Identity: Endotherial_cell not present in group su012_pre. Skipping su012_pre” Testing group su005_pre: (Endotherial_cell) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Myofibroblast) Testing group su005_post: (Endotherial_cell) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Myofibroblast, Malignant_cell) Testing group su006_post: (Endotherial_cell) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast) Warning message: “Identity: Endotherial_cell not present in group su009_pre. Skipping su009_pre” Warning message: “Identity: Endotherial_cell not present in group su009_post. Skipping su009_post” Testing group su008_post: (Endotherial_cell) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Myofibroblast) Testing group su006_pre: (Endotherial_cell) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Myofibroblast) Testing group su001_post: (Endotherial_cell) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Myofibroblast, CD8_Tcell5, Malignant_cell) Warning message: “Identity: Myofibroblast not present in group su010_pre. Skipping su010_pre” Testing group su002_pre: (Myofibroblast) vs (Macrophage, CD4_Tcell1, Dendritic_cell, NK_cell, Malignant_cell, CD8_Tcell2, CD8_Tcell6, CD4_Tcell4, CD4_Tcell5, Fibroblast, Plasma_cell, CD8_Tcell4, CD4_Tcell3, CD4_Tcell2, CD8_Tcell3, CD8_Tcell1, CD8_Tcell5, Endotherial_cell) Testing group su002_post: (Myofibroblast) vs (CD8_Tcell4, CD4_Tcell2, CD4_Tcell1, CD8_Tcell1, CD8_Tcell3, CD4_Tcell3, CD8_Tcell2, CD4_Tcell4, Bcell, CD4_Tcell5, CD8_Tcell6, Plasma_cell, Fibroblast, NK_cell, Dendritic_cell, Endotherial_cell, Macrophage, Plasmacytoid_dendritic_cell) Testing group su003_pre: (Myofibroblast) vs (CD8_Tcell2, CD4_Tcell2, CD8_Tcell4, Fibroblast, Malignant_cell, CD4_Tcell4, CD4_Tcell1, Macrophage, CD4_Tcell3, CD8_Tcell1, NK_cell, Plasmacytoid_dendritic_cell, Dendritic_cell, CD8_Tcell6, Endotherial_cell, Plasma_cell, CD8_Tcell3, CD4_Tcell5, CD8_Tcell5) Testing group su007_post: (Myofibroblast) vs (Dendritic_cell, CD8_Tcell1, Bcell, CD8_Tcell2, CD4_Tcell5, CD4_Tcell1, CD4_Tcell3, CD8_Tcell4, CD4_Tcell4, Malignant_cell, CD8_Tcell3, Plasma_cell, NK_cell, Endotherial_cell, CD8_Tcell6, CD4_Tcell2, Macrophage, Fibroblast, CD8_Tcell5) Warning message: “Identity: Myofibroblast not present in group su010_post. Skipping su010_post” Testing group su004_pre: (Myofibroblast) vs (CD8_Tcell2, CD8_Tcell3, CD4_Tcell4, CD4_Tcell5, CD4_Tcell3, CD8_Tcell1, CD4_Tcell1, CD4_Tcell2, CD8_Tcell4, Bcell, NK_cell, CD8_Tcell6, Dendritic_cell, Macrophage, Fibroblast, Endotherial_cell, Malignant_cell, Plasmacytoid_dendritic_cell, Plasma_cell) Warning message: “Identity: Myofibroblast not present in group su012_post. Skipping su012_post” Testing group su004_post: (Myofibroblast) vs (CD8_Tcell2, CD4_Tcell4, CD4_Tcell5, CD4_Tcell1, CD4_Tcell2, Macrophage, CD4_Tcell3, CD8_Tcell1, CD8_Tcell3, CD8_Tcell6, NK_cell, CD8_Tcell5, CD8_Tcell4, Dendritic_cell, Fibroblast, Plasmacytoid_dendritic_cell, Malignant_cell, Bcell, Plasma_cell, Endotherial_cell) Testing group su003_post: (Myofibroblast) vs (Malignant_cell, Dendritic_cell, Fibroblast, CD4_Tcell1, Macrophage, CD8_Tcell4, CD4_Tcell2, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell5, NK_cell, Endotherial_cell, CD8_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell2, Bcell, CD4_Tcell3, CD4_Tcell5, Plasma_cell) Testing group su001_pre: (Myofibroblast) vs (Malignant_cell, CD4_Tcell5, Dendritic_cell, NK_cell, CD4_Tcell1, Macrophage, Endotherial_cell, CD4_Tcell2, Fibroblast, CD8_Tcell3, CD8_Tcell1, CD4_Tcell4, CD4_Tcell3, CD8_Tcell4, CD8_Tcell6, Plasmacytoid_dendritic_cell, CD8_Tcell2, Plasma_cell, CD8_Tcell5, Bcell) Testing group su007_pre: (Myofibroblast) vs (CD4_Tcell1, CD8_Tcell2, CD4_Tcell3, CD4_Tcell4, CD8_Tcell1, CD8_Tcell4, CD4_Tcell5, CD8_Tcell3, CD4_Tcell2, NK_cell, CD8_Tcell5, CD8_Tcell6, Macrophage, Malignant_cell, Dendritic_cell, Plasma_cell, Plasmacytoid_dendritic_cell, Fibroblast, Endotherial_cell, Bcell) Testing group su008_pre: (Myofibroblast) vs (Plasmacytoid_dendritic_cell, Plasma_cell, Dendritic_cell, Malignant_cell, Bcell, NK_cell, Macrophage, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell1, Fibroblast, CD8_Tcell1, CD8_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell2, CD4_Tcell3, CD4_Tcell4, Endotherial_cell) Warning message: “Identity: Myofibroblast not present in group su012_pre. Skipping su012_pre” Testing group su005_pre: (Myofibroblast) vs (Macrophage, CD8_Tcell5, CD4_Tcell1, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, NK_cell, Malignant_cell, Plasma_cell, CD4_Tcell3, CD8_Tcell2, Bcell, CD4_Tcell4, CD8_Tcell3, Fibroblast, CD8_Tcell6, CD8_Tcell1, CD4_Tcell2, CD4_Tcell5, Endotherial_cell) Testing group su005_post: (Myofibroblast) vs (CD4_Tcell1, CD8_Tcell3, CD8_Tcell6, CD4_Tcell5, CD4_Tcell4, CD8_Tcell2, CD4_Tcell3, CD8_Tcell1, CD8_Tcell4, NK_cell, CD4_Tcell2, CD8_Tcell5, Dendritic_cell, Bcell, Macrophage, Plasma_cell, Fibroblast, Plasmacytoid_dendritic_cell, Endotherial_cell, Malignant_cell) Testing group su006_post: (Myofibroblast) vs (Macrophage, Plasma_cell, Dendritic_cell, CD8_Tcell5, Plasmacytoid_dendritic_cell, CD8_Tcell6, CD8_Tcell4, Bcell, Fibroblast, NK_cell, CD4_Tcell1, CD8_Tcell3, CD4_Tcell2, CD8_Tcell2, CD8_Tcell1, CD4_Tcell3, CD4_Tcell4, CD4_Tcell5, Malignant_cell, Endotherial_cell) Testing group su009_pre: (Myofibroblast) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell5, CD8_Tcell6, CD4_Tcell3, Malignant_cell, CD8_Tcell2, CD8_Tcell3, Dendritic_cell, CD4_Tcell4, CD4_Tcell1, NK_cell, CD4_Tcell5, Fibroblast, CD8_Tcell4, Plasmacytoid_dendritic_cell, Macrophage, Plasma_cell, Bcell) Testing group su009_post: (Myofibroblast) vs (CD8_Tcell1, CD8_Tcell2, NK_cell, CD8_Tcell5, CD4_Tcell1, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, Malignant_cell, CD4_Tcell2, CD8_Tcell4, CD4_Tcell4, CD8_Tcell6, Fibroblast, Macrophage, Dendritic_cell, Plasma_cell, Bcell, Plasmacytoid_dendritic_cell) Testing group su008_post: (Myofibroblast) vs (CD8_Tcell2, CD4_Tcell3, CD4_Tcell1, NK_cell, CD8_Tcell1, CD8_Tcell3, CD8_Tcell5, CD8_Tcell4, CD4_Tcell2, CD4_Tcell5, CD8_Tcell6, CD4_Tcell4, Fibroblast, Macrophage, Malignant_cell, Plasma_cell, Dendritic_cell, Plasmacytoid_dendritic_cell, Bcell, Endotherial_cell) Testing group su006_pre: (Myofibroblast) vs (Plasma_cell, Macrophage, CD8_Tcell5, CD4_Tcell1, Bcell, Dendritic_cell, CD8_Tcell4, Plasmacytoid_dendritic_cell, Fibroblast, CD8_Tcell6, CD8_Tcell2, NK_cell, CD8_Tcell3, CD4_Tcell3, CD8_Tcell1, CD4_Tcell2, CD4_Tcell4, CD4_Tcell5, Endotherial_cell, Malignant_cell) Testing group su001_post: (Myofibroblast) vs (CD8_Tcell1, CD4_Tcell2, CD8_Tcell3, CD4_Tcell3, CD4_Tcell5, CD4_Tcell4, CD8_Tcell6, CD8_Tcell2, NK_cell, CD4_Tcell1, Bcell, CD8_Tcell4, Macrophage, Dendritic_cell, Plasmacytoid_dendritic_cell, Plasma_cell, Fibroblast, Endotherial_cell, CD8_Tcell5, Malignant_cell)